What is your budget, and what do you need?
What is in your current pc?
1) One of the best productive upgrades to a pc is the addition of a second monitor.
Preferably it should be the same size and resolution as your current one, assuming you like your current monitor.
2) You are probably using IDE based hard drive/s. They are SLOW.
Base your new pc on a SSD of some size. You will be amazed at how quick your pc will feel. 80gb should be fine for the os, some files and apps. Expect to pay $1.50 for a good one.
Look for Intel, Samsung, or crucial, in that order for reliability.
From a practical performance point of view(ie; not synthetic benchmarks) all current SSD's will perform similarly in normal activities.If you have a requirement for lots of hard drive data, then add one in whatever capacity you need.
3) A good dual core cpu will be plenty, unless you are running heavily multithreaded apps. A sandy bridge G850 will do the job for <$100.
4) The integrated graphics will do fine for dual monitors.
5) There is no need for large ATX motherboards. Look at M-ATX, or even m-ITX if case size might be an issue.